Faulconer

Tree Position

Unique Mutations

The mutations unique to this man are summarized in the table below. Those with a '+' or '*' confidence level are considered by FamilyTreeDNA or FullGenomesCorp to be high quality SNPs/INDELs. For completeness, all other mutations of lesser confidence are included as well. These additional mutations may be useful for distinguishing between very closely related men.

Occasionally, some of the mutations listed here will be thought to be shared with other men in which case they might appear in upstream blocks on the tree. When this happens, the 'Blocks' field will indicate what block they appear in. Such a situation might arise with BigY men if the BED data suggests another man may be positive for a SNP, even though it doesn't appear in his VCF data. It might also happen if Chromo2 testing or Sanger sequencing of other men not on the tree show the SNP to be shared.

POS-REF-ALT (hg19)

POS-REF-ALT (hg38)

Blocks

Names

Region

McDonald BED

combBED

STR

FTDNAN43634

16252782-T-C

14140902-T-C

Y13844 Z21737

Y

Y

+

21973658-G-A

19811772-G-A

Y13848 Z21749

Y

Y

+

7555859-C-T

7687818-C-T

Y13215 Z21729

Y

Y

+

8032787-C-T

8164746-C-T

Y13216 Z21730

Y

Y

+

8142418-A-T

8274377-A-T

Y13217 Z21731

Y

Y

+

21422605-C-A

19260719-C-A

Y

Y

+

8480188-C-T

8612147-C-T

Y13836 Z21733

Y

Y

+

8674341-G-A

8806300-G-A

Y13219 Z21734

Y

Y

+

9737441-C-T

9899832-C-T

Y13837 Z21735

IR3_Prx

+

15307522-T-TCTCCC

13195624-T-TCTCCC

5×CTCCC

+

15320664-G-GGAAGAAGAAGAAGAAGAA

13208770-G-GGAAGAA

18×GAA

+

15670386-T-C

13558506-T-C

Y13220 Z21736

Y

+

16252786-TC-T

14140906-TC-T

+

6872457-C-T

7004416-C-T

Y

Y

+

16360920-A-G

14249040-A-G

S8139

Y

Y

+

16544788-G-T

14432908-G-T

Y13222 Z21739

Y

Y

+

16719314-T-G

14607434-T-G

Y13223 Z21740

Y

Y

+

16897014-A-G

14785134-A-G

Y13224 Z21741

Y

Y

+

17573541-A-G

15461661-A-G

Y13225 Z21742

Y

Y

+

17869267-C-A

15757387-C-A

Y13841 Z21743

Y

Y

+

19120044-A-T

17008164-A-T

Y13846 Z21744

Y

Y

+

19243075-AG-A

17131195-AG-A

+

19360564-C-A

17248684-C-A

Y13847 Z21746

Y

Y

+

19397208-TTCTA-T

17285328-TTCTA-T

+

21687582-A-T

19525696-A-T

Y

Y

+

6995607-T-G

7127566-T-G

Y13843 Z21728

Y

Y

+

8231493-G-A

8363452-G-A

Y13218 Z21732

Y

Y

+

3545293-G-T

3677252-G-T

Y13835 Z21727

+

22487356-G-A

20325470-G-A

DYZ19

+

24422366-G-A

22276219-G-A

Y13838 Z21753

Y

+

23799902-A-T

21638016-A-T

Y13849 Z21752

Y

+

23297025-C-A

21135139-C-A

S8137

Y

Y

+

21560112-GT-G

19398226-GT-G

+

22459548-C-T

20297662-C-T

Z21750

DYZ19

+

22478818-A-T

20316932-A-T

Z21751

DYZ19

+

22537242-T-A

20375356-T-A

PF2193

**

22424387-G-C

20262501-G-C

DYZ19

**

13196297-T-C

11040621-T-C

PF465

**

13454779-A-T

11299103-A-T

**

14506747-C-A

12394952-C-A

**

22236337-T-TCA

20074451-T-TCA

DYZ19

**

10008575-G-A

10170966-G-A

**

22329346-C-T

20167460-C-T

DYZ19

**

22280073-C-A

20118187-C-A

DYZ19

***

26148615-T-G

24002468-T-G

P1_Y1

***

13696283-G-A,C

11540607-G-A,C

***

19948181-C-CCCTTCTTTCTTTCTTT,CCTTTCTTTCTTTCTTT

17836301-C-CCCTTCTTTCTTTCTTT,CCTTTCTTTCTTTCTTT

P5_Prx

21×CTTT

***

58979446-TCCATTCCATG-T,TCCATTCCATT

56833299-TCCATTCCATG-T,TCCATTCCATT

***

58975667-C-T

56829520-C-T

***

28813318-T-G

26667171-T-G

***

28795943-A-T

26649796-A-T

***

27714328-CTTT-C

25568181-CTTT-C

P1_Y2

15×T

***

26398338-C-T

24252191-C-T

P1_Y1

***

26142904-T-G

23996757-T-G

P1_Y1

***

22275949-G-C

20114063-G-C

DYZ19

***

25818140-A-G

23671993-A-G

P1_b3

***

25461433-C-CTTTTT

23315286-C-CTTTTT

P2_r2

26×T

***

22309818-G-T

20147932-G-T

DYZ19

***

22304966-G-T

20143080-G-T

DYZ19

***

22234532-A-T

20072646-A-T

DYZ19

***

22289715-G-A

20127829-G-A

DYZ19

***

22241407-A-T

20079521-A-T

DYZ19

***

22260214-C-T

20098328-C-T

DYZ19

***

22269929-T-G

20108043-T-G

DYZ19

***

22430925-G-T

20269039-G-T

DYZ19

***

13862226-G-A

11741520-G-A

***

20048466-C-T

17936586-C-T

P5_Prx

***

58974136-A-G

56827989-A-G

***

13820826-ATGGAT-A

11700120-ATGGAT-A

***

58975664-T-TTCCATTCCATTCCAG

56829517-T-TTCCATTCCATTCCAG

***

13748501-T-G

11592825-T-G

***

13455619-T-A

11299943-T-A

***

13455195-A-G

11299519-A-G

***

19411914-A-AAAAG,G

17300034-A-AAAAG,G

14×AAAG

***

13804754-G-A

11684048-G-A

***

19815544-A-T

17703664-A-T

P5_Prx

***

13804747-GAATTT-G

11684041-GAATTT-G

***

13676615-A-T

11520939-A-T

***

13451890-T-C

11296214-T-C

***

10024581-TC-T

10186972-TC-T

***

28795928-T-A

26649781-T-A

***

13464398-C-T

11308722-C-T

***

22232040-C-A

20070154-C-A

BY10784

DYZ19

***

26235428-C-T

24089281-C-T

P1_Y1

***

20033954-G-A

17922074-G-A

P5_Prx

***

13728447-C-G

11572771-C-G

***

19792750-G-A

17680870-G-A

P5_Prx

***

13858477-C-A,G

11737771-C-A,G

***

13851112-GAATCC-G

11730406-GAATCC-G

***

13850342-G-A

11729636-G-A

***

13728464-G-C

11572788-G-C

***

13728448-A-T

11572772-A-T

***

13728441-A-G

11572765-A-G

***

13447214-C-G

11291538-C-G

***

13728439-G-A

11572763-G-A

***

13728428-TGCAATC-T

11572752-TGCAATC-T

***

13728427-A-C

11572751-A-C

***

13648954-GAATGT-G

11493278-GAATGT-G

***

9179156-G-C

9341547-G-C

***

3131531-C-CTTCTCTTCT

3263490-C-CTTCTCTTCT

***

13451887-C-T

11296211-C-T

***

13141225-A-C,T

10630711-A-C,T

***

In the table above, the meaning of the confidence field depends on whether the data comes from an FTDNA kit or an FGC kit. For FTDNA kits, + implies a "PASS" result with just one possible variant, * indicates a "PASS" but with multiple variants, ** indicates "REJECTED" with just a single variant, and *** indicates "REJECTED" with multiple possible variants. 'A*' are heterozygous variants not called by FTDNA, but still pulled from the VCF file. For FGC kits, + indicates over 99% likely genuine (95% for INDELs); * over 95% likely genuine (90% for INDELs); ** about 40% likely genuine; *** about 10% likely genuine. Manual entries read directly from a BAM file will be either + indicating positive, or * indicating that the data show a mixture of possible variants.

For the FTDNA kits, the BED data is encoded in the background color of the cells. Those cells with a white background have coverage, those with a grey background indicate no coverage in the BED file, and those with a pink background indicate the mutation is on the edge of a coverage region. These pink regions often indicate that the individual may be positive for a SNP even if there is no corresponding entry in the vcf file.

The McDonald BED column indicates whether or not the mutation is a SNP and falls in the BED region used by Dr. Iain McDonald in the age analysis he does for R-U106 men.

Haplotype Progression

The data below reveals the progression of changes in the haplotype. The bottom row is the haplotype for this man and above him are the inferred ancestral haplotypes for various upstream blocks. These inferred haplotypes are very much a work in progress, and any suggested modifications are appreciated. I think we can use our vast collection of haplotype data to refine these haplotypes. Mutations made from each upstream block are shown in sequence. The cell color is determined by the block in which the mutation took place.